Plants require nitrogen, phosphorus and certain other essential elements to survive and grow. Most fertilizers include both nitrogen, in the form of ammonium or nitrates, and phosphorus. However, not all of a fertilizer used in farming is taken up by the crops. A fair amount of the fertilizer is washed away and contaminates the ground water in the surrounding community. In addition, supplementing soil nutrients with fertilizer increases the cost to produce a crop. Nitrogen in the atmosphere represents a good source for nitrogen given its abundance. But only prokaryotes are able to “fix” atmospheric nitrogen into a form usable by plants. Certain plants, legumes in particular, have evolved a symbiotic relationship with nitrogen fixing bacteria. Such plants are often planted to replenish the soils for other crops. In addition, some of the same proteins that are involved in establishing this symbiosis also participate in establishing symbiosis with mycorrhizal fungi that assist in utilization of phosphorus. Thus there is a need for methods of enhancing a plant's symbiotic machinery to reduce the need for supplementing soil with added nutrients. In addition, there is a need for methods and compositions that enhance the nutrients in the soil directly such as addition of bacteria that fix nitrogen in the absence of symbiosis with plants to lower costs associated with fertilizing during farming.